Skip to main content

Table 8 Average speed in GO concept pairs per second (pairs/s) for the evaluation of two representative ontology-based similarity measures based on the Gene Ontology [1, 2] (2020-05-02 version, 44509 nodes)) implemented by state-of-the-art SML [34] library and HESML

From: HESML: a real-time semantic measures library for the biomedical domain with a reproducible survey

Similarity measure

Measure type

SML

HESML

Avg. speed

(pairs/s)

Avg. speed

(pairs/s)

Rada [71]

Edge-counting

0.077 (20)

3.217 (20)

AncSPL-Rada

(this work)

Edge-counting

–

140422 \((10^7)\)

Lin-Seco [87, 110]

IC model

IC-based

372140 \((10^7)\)

1063219 \((10^7)\)

  1. Best performing values are shown in bold. The number of random GO concept pairs evaluated to measure each value is shown between parentheses